0. Annotate cell types for all the cells
mkdir -p example/cfa
[ -f example/cfa/psych.annot.gz ] || \
../src/mmutil_annotate_col \
--mtx data/brain_2018-05-03/filtered_count_matrix.mtx.gz \
--row data/brain_2018-05-03/features.tsv.gz \
--col data/brain_2018-05-03/barcodes.tsv.gz \
--ann PsychENCODE.marker \
--batch_size 1000 \
--out example/cfa/psych
2. Create another file set for COCOA analysis
# Expected: input.{mtx,cols}.gz
# Column order may change
[ -f example/cfa/input.mtx.gz ] || \
../src/mmutil_select_col \
data/brain_2018-05-03/filtered_count_matrix.mtx.gz \
data/brain_2018-05-03/filtered_count_matrix.cols.gz \
example/cfa/input.tags.gz \
example/cfa/input
############################################################
## prepare for the input files matching the same order of ##
## cells/columns ##
############################################################
.hdr <- "example/cfa/input"
.trt.file <- .hdr %&% ".trt.gz"
.ind.file <- .hdr %&% ".ind.gz"
.annot.file <- .hdr %&% ".annot.gz"
.lab.file <- .hdr %&% ".lab.gz"
if(any(!file.exists(.trt.file, .annot.file, .ind.file, .lab.file))) {
cols.dt <- .fread("example/cfa/input.cols.gz") %>%
(function(x){ colnames(x)=c("TAG"); x }) %>%
left_join(meta.pheno.dt) %>%
left_join(annot.dt)
xx = cols.dt[, .(np_sqrt, nft_sqrt)]
y.pheno <- data.table(y = predict(prop.model, xx)) %>%
mutate(y = if_else(y > 0, "AD", "HC"))
ind.dt <- cols.dt[, .(projid)] %>%
mutate(y = unlist(y.pheno)) %>%
mutate(ind = projid %&% "_" %&% y)
.fwrite(ind.dt[, .(ind)], "example/cfa/input.ind.gz")
.fwrite(y.pheno, "example/cfa/input.trt.gz")
.fwrite(cols.dt[, .(TAG, celltype)], "example/cfa/input.annot.gz")
.fwrite(cols.dt[, .(celltype)] %>% unique, "example/cfa/input.lab.gz")
}
3. Run the counterfactual adjustment model
# Just to have this in the same location
[ -f example/cfa/input.rows.gz ] || \
cp data/brain_2018-05-03/filtered_gene_row_names.txt.gz \
example/cfa/input.rows.gz
# Basic aggregate statistics
[ -f example/cfa/output.sum.gz ] || \
../src/mmutil_aggregate_col \
--mtx example/cfa/input.mtx.gz \
--col example/cfa/input.cols.gz \
--annot example/cfa/input.annot.gz \
--lab example/cfa/input.lab.gz \
--ind example/cfa/input.ind.gz \
--out example/cfa/output
# CF-adjusted aggregate statistics
[ -f example/cfa/output.resid_mu.gz ] || \
../src/mmutil_cfa_col \
--mtx example/cfa/input.mtx.gz \
--col example/cfa/input.cols.gz \
--annot example/cfa/input.annot.gz \
--trt example/cfa/input.trt.gz \
--lab example/cfa/input.lab.gz \
--ind example/cfa/input.ind.gz \
--knn 10 --rank 30 --bilink 100 --log_scale --normalize \
--out example/cfa/output
MIN.TOT.CUTOFF <- 50
.data.file <- "example/cfa/stat_tab.rdata"
if(!file.exists(.data.file)) {
stat.tab <- .read.stat.all("example/cfa/output", tot.cutoff = MIN.TOT.CUTOFF)
save(stat.tab, file = .data.file)
} else {
load(.data.file)
}
stat.avg.tab <- .take.average(stat.tab, "AD", tot.cutoff = MIN.TOT.CUTOFF)
First, show confounders and genes associated with the confounding effects
.mat <- stat.tab[tot > 0, .(mu=sum(cf.mu)), by=.(gene, col)] %>%
spread(key=col, value=mu, fill=0)
.ln.mat <- log(1 + .mat[, -"gene"]) %>% as.matrix %>% t %>% scale
.ln.mat[is.na(.ln.mat)] <- 0
gene.cf.assoc.dt <- test.gene.association(.ln.mat) %>%
na.omit %>%
rename(cf.beta = beta, cf.se = se, cf.pv = p.val) %>%
as.data.table
top.genes <-
gene.cf.assoc.dt[order(gene.cf.assoc.dt$cf.pv),
head(.SD, 3),
by = .(pheno, celltype)] %>%
filter(cf.pv < 5e-4) %>%
select(gene) %>% unique %>% unlist
top.cf.assoc.dt <- gene.cf.assoc.dt[gene %in% top.genes] %>%
na.omit %>%
mutate(row = gene) %>%
mutate(col = pheno %&% "@" %&% celltype) %>%
mutate(weight = -log10(pmax(cf.pv, 1e-8))) %>%
order.pair(ret.tab = TRUE) %>%
as.data.table
## Loading required package: cba
## Loading required package: proxy
##
## Attaching package: 'proxy'
## The following objects are masked from 'package:stats':
##
## as.dist, dist
## The following object is masked from 'package:base':
##
## as.matrix
plt <-
.gg.plot(top.cf.assoc.dt, aes(y=row, x=col, fill=celltype, size=weight)) +
theme(title = element_text(size=8)) +
theme(axis.text.x = element_blank()) +
theme(axis.ticks.x = element_blank()) +
theme(axis.title = element_blank()) +
ggtitle("Top " %&% length(top.genes) %&% " genes ~ confounding effects") +
facet_grid(.~pheno, scales="free", space="free") +
geom_point(pch=22, stroke=.1) +
scale_fill_brewer(palette = "Paired") +
scale_size_continuous("p-value",
range=c(0,3),
labels = function(x) num.sci(10^(-x)))
.file <- fig.dir %&% "/Fig_Confounding_Genes.pdf"
.gg.save(filename = .file, plot = plt, width=5, height=5)
print(plt)

PDF
.row.df <- match.row.with.pheno(.ln.mat)
.tsne <- Rtsne::Rtsne(.ln.mat, n_threads=16)
colnames(.tsne$Y) <- "tSNE" %&% 1:ncol(.tsne$Y)
.tsne.dt <- cbind(.row.df, .tsne$Y) %>% as.data.table
p1 <- .gg.plot(.tsne.dt, aes(x=tSNE1, y=tSNE2)) +
theme(legend.position=c(1,1), legend.justification = c(1,1)) +
geom_point(aes(fill=celltype), alpha=.8, stroke=.2, size=1.25, pch=21) +
scale_fill_brewer("", palette = "Paired")
p2 <- .gg.plot(.tsne.dt %>% arrange(desc(disease)), aes(x=tSNE1, y=tSNE2)) +
theme(legend.position=c(1,1), legend.justification = c(1,1)) +
geom_point(aes(fill=disease), alpha=.5, stroke=.2, size=1.25, pch=21) +
scale_fill_manual("", values=c("#FF9999","#FFFFFF"))
plt <- p1 | p2
.file <- fig.dir %&% "/Fig_Confounding_tSNE.pdf"
.gg.save(filename = .file, plot = plt, width=6, height=4)
print(plt)

PDF
Global statistics
.file <- fig.dir %&% "/Fig_histogram_pvalue.pdf"
pdf(.file, width = 4, height = 4)
hist(stat.avg.tab$pv.z, main="", xlab="gene-level p-value")
dev.off()
## quartz_off_screen
## 2
hist(stat.avg.tab$pv.z, main="", xlab="gene-level p-value")

PDF
Marginal statistics without confounding factor adjustment
gene.obs.assoc.dt <-
stat.tab[, .(mu=sum(tot)), by=.(gene, col)] %>%
spread(key=col, value=mu, fill=0) %>%
(function(x) log(1 + x[, -"gene"])) %>%
(function(x) scale(t(as.matrix(x)))) %>%
(function(x) { x[is.na(x)] <- 0; x }) %>%
test.gene.association %>%
na.omit %>%
rename(obs.beta = beta, obs.se = se, obs.pv = p.val) %>%
as.data.table
gene.assoc.dt <- stat.avg.tab %>% na.omit %>%
merge(gene.ontology$coding, by.x = "gene", by.y = "hgnc_symbol")
gene.assoc.dt <- gene.assoc.dt[order(gene.assoc.dt$pv.z),
head(.SD, 1),
by=.(gene, celltype)]
gene.assoc.dt <- gene.assoc.dt %>%
left_join(gene.obs.assoc.dt[pheno=="pathoAD"], by = c("gene", "celltype")) %>%
left_join(gene.cf.assoc.dt[pheno=="pathoAD"], by = c("gene", "celltype", "pheno"))
PV.CUTOFF <- 0.05/nrow(gene.assoc.dt)
plot.genome.view <- function(ct, .tot.dt, .cutoff){
.chr.names <- c(as.character(1:22), "X", "Y", "MT")
.dt <- .tot.dt[celltype == ct & chromosome_name %in% .chr.names] %>%
mutate(chr = factor(chromosome_name, .chr.names)) %>%
mutate(z.trunc = pmin(pmax(z, -4), 4))
.dt.show <- .dt[pv.z < .cutoff & abs(ln.mu) > .1]
.dt.show.lab <- .dt.show[order(.dt$pv.z), head(.SD, 3), by=.(chr)] %>%
filter(nchar(gene) > 0) %>%
na.omit
x.lab.fn <- function(x) num.int(x/1e6)
y.lab.fn <- function(x) num.sci(10^(-x))
.aes <- aes(x=transcript_start,
y=-log10(pmax(pv.z, 1e-30)),
fill=z.trunc)
ret <-
.gg.plot(.dt, .aes) +
ggtitle(ct) +
theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1, size = 5)) +
theme(title = element_text(size=8)) +
theme(strip.text = element_text(size=6)) +
facet_grid(. ~ chr, scales="free", space="free") +
geom_hline(yintercept=-log10(.cutoff), size=.1, col="red") +
scale_x_continuous(labels=x.lab.fn) +
scale_y_continuous(labels=y.lab.fn) +
ylab("p-value") + xlab("genomic locations (mb)") +
scale_fill_gradient2(low="blue", high="red", guide=FALSE) +
geom_point(pch=19, col="gray60", size=.5)
if(nrow(.dt.show) > 0){
ret <- ret + geom_point(data = .dt.show, pch=21)
}
if(nrow(.dt.show.lab) > 0){
ret <- ret +
ggrepel::geom_text_repel(data = .dt.show.lab, aes(label = gene), size = 1)
}
return(ret)
}
.ct.valid <- gene.assoc.dt[pv.z < PV.CUTOFF & abs(ln.mu) > .1] %>%
na.omit %>%
select(celltype) %>%
unique %>%
unlist
p.list <-
setdiff(.ct.valid, c("Per","Endo")) %>%
lapply(plot.genome.view, .tot.dt = gene.assoc.dt, .cutoff = PV.CUTOFF)
plt <- wrap_plots(p.list, ncol = 1)
.file <- fig.dir %&% "/Fig_Genome_View.pdf"
.gg.save(filename = .file, plot = plt, width=8, height=8)
print(plt)

PDF
Significant genes
.cell.count <- .fread("example/cfa/input.annot.gz") %>%
(function(x) { colnames(x) <- c("TAG", "celltype"); x }) %>%
(function(x) x[, .(Cell = .N), by=.(celltype)]) %>%
(function(x) x[, p.Cell := 100*Cell/sum(Cell)])
.gene.count <-
.gene.table[, .(Gene = .N), by = .(celltype)] %>%
(function(x) x[, p.Gene := 100*Gene/sum(Gene)])
.aes.cell <- aes(y=celltype, yend=celltype, x=0, xend=-Cell, colour = celltype, label=num.int(Cell) %&% " (" %&% num.round(p.Cell) %&% "%)")
.aes.gene <- aes(y=celltype, yend=celltype, x=0, xend=Gene, colour = celltype, label=num.int(Gene) %&% " (" %&% num.round(p.Gene) %&% "%)")
.plt <- function(.df, .aes) {
.gg.plot(.df, .aes) +
theme(axis.ticks.y = element_blank()) +
theme(axis.title.y = element_blank()) +
xlab("number of cells") +
geom_segment(size=10) +
ggrepel::geom_text_repel(size=2.5, colour = "gray20") +
scale_x_continuous(labels=function(x) num.int(abs(x))) +
scale_colour_brewer(palette = "Paired", guide = FALSE)
}
plt <- ((.plt(.cell.count, .aes.cell) + scale_y_discrete(position="right")) |
.plt(.gene.count, .aes.gene))
.file <- fig.dir %&% "/Fig_Num_Discovery.pdf"
.gg.save(filename = .file, plot = plt, width=4, height=3)
print(plt)

PDF
|
celltype
|
gene
|
N
|
Chr
|
TSS
|
TES
|
FC
|
SD
|
Z
|
P
|
|
Astro
|
GFAP
|
1,609
|
17
|
44,903
|
44,917
|
1.38
|
0.03
|
12.86
|
7.7e-38
|
|
Astro
|
CHI3L1
|
687
|
1
|
203,178
|
203,187
|
1.50
|
0.06
|
10.85
|
2.0e-27
|
|
Astro
|
MT2A
|
2,899
|
16
|
56,608
|
56,610
|
1.19
|
0.02
|
9.27
|
1.9e-20
|
|
Astro
|
PRKG1
|
2,617
|
10
|
50,990
|
52,299
|
1.19
|
0.02
|
9.14
|
6.2e-20
|
|
Astro
|
HSP90AA1
|
1,342
|
14
|
102,080
|
102,140
|
1.27
|
0.03
|
8.92
|
4.6e-19
|
|
Astro
|
DPP10
|
3,236
|
2
|
114,442
|
115,846
|
1.16
|
0.02
|
8.64
|
5.8e-18
|
|
Astro
|
NEBL
|
3,438
|
10
|
20,779
|
21,294
|
1.15
|
0.02
|
8.44
|
3.2e-17
|
|
Astro
|
CPE
|
3,396
|
4
|
165,361
|
165,499
|
1.15
|
0.02
|
8.32
|
9.0e-17
|
|
Astro
|
AQP1
|
208
|
7
|
30,911
|
30,926
|
1.66
|
0.11
|
7.66
|
1.8e-14
|
|
Astro
|
ADCY2
|
2,802
|
5
|
7,396
|
7,831
|
1.15
|
0.02
|
7.58
|
3.5e-14
|
|
Astro
|
TRPM3
|
2,971
|
9
|
70,529
|
71,447
|
1.15
|
0.02
|
7.53
|
4.9e-14
|
|
Astro
|
CLU
|
4,400
|
8
|
27,596
|
27,615
|
1.11
|
0.02
|
7.10
|
1.2e-12
|
|
Astro
|
SNED1
|
303
|
2
|
240,998
|
241,096
|
1.48
|
0.08
|
7.01
|
2.5e-12
|
|
Astro
|
RGS6
|
286
|
14
|
71,932
|
72,567
|
1.48
|
0.08
|
6.79
|
1.1e-11
|
|
Astro
|
GJA1
|
2,458
|
6
|
121,435
|
121,450
|
1.14
|
0.02
|
6.71
|
1.9e-11
|
|
Astro
|
DST
|
3,121
|
6
|
56,457
|
56,955
|
1.13
|
0.02
|
6.68
|
2.4e-11
|
|
Astro
|
HSPB1
|
650
|
7
|
76,302
|
76,305
|
1.28
|
0.05
|
6.46
|
1.0e-10
|
|
Astro
|
RPS25
|
363
|
11
|
119,015
|
119,019
|
1.38
|
0.07
|
6.36
|
2.1e-10
|
|
Astro
|
ITGB4
|
499
|
17
|
75,721
|
75,758
|
1.32
|
0.06
|
6.33
|
2.5e-10
|
|
Astro
|
FYN
|
1,939
|
6
|
111,660
|
111,874
|
1.15
|
0.03
|
6.24
|
4.3e-10
|
|
Astro
|
RASGEF1B
|
1,827
|
4
|
81,426
|
82,045
|
1.15
|
0.03
|
6.09
|
1.1e-09
|
|
Astro
|
CD44
|
184
|
11
|
35,138
|
35,233
|
1.52
|
0.11
|
5.98
|
2.2e-09
|
|
Astro
|
LINGO1
|
1,706
|
15
|
77,613
|
77,821
|
1.15
|
0.03
|
5.81
|
6.2e-09
|
|
Astro
|
VCAN
|
242
|
5
|
83,471
|
83,583
|
1.43
|
0.09
|
5.74
|
9.4e-09
|
|
Astro
|
HSPA1A
|
559
|
6
|
31,815
|
31,818
|
1.26
|
0.05
|
5.61
|
2.0e-08
|
|
Astro
|
RFX4
|
1,641
|
12
|
106,583
|
106,763
|
1.15
|
0.03
|
5.60
|
2.2e-08
|
|
Astro
|
PTGDS
|
2,893
|
9
|
136,975
|
136,982
|
1.11
|
0.02
|
5.52
|
3.5e-08
|
|
Astro
|
CRYAB
|
500
|
11
|
111,908
|
111,924
|
1.27
|
0.06
|
5.49
|
4.0e-08
|
|
Astro
|
MAPK4
|
1,034
|
18
|
50,560
|
50,732
|
1.18
|
0.04
|
5.44
|
5.2e-08
|
|
Astro
|
PLEKHA5
|
562
|
12
|
19,129
|
19,377
|
1.25
|
0.05
|
5.43
|
5.5e-08
|
|
Astro
|
GPM6B
|
2,651
|
X
|
13,770
|
13,939
|
1.11
|
0.02
|
5.42
|
5.9e-08
|
|
Astro
|
FAM171A1
|
888
|
10
|
15,211
|
15,372
|
1.20
|
0.04
|
5.41
|
6.4e-08
|
|
Astro
|
PLEC
|
442
|
8
|
143,915
|
143,977
|
1.28
|
0.06
|
5.31
|
1.1e-07
|
|
Astro
|
CNTN1
|
1,818
|
12
|
40,692
|
41,073
|
1.13
|
0.03
|
5.30
|
1.2e-07
|
|
Astro
|
AEBP1
|
318
|
7
|
44,104
|
44,115
|
1.33
|
0.07
|
5.29
|
1.2e-07
|
|
Astro
|
TPT1
|
335
|
13
|
45,333
|
45,342
|
1.32
|
0.07
|
5.28
|
1.3e-07
|
|
Astro
|
MT1E
|
1,330
|
16
|
56,625
|
56,628
|
1.15
|
0.03
|
5.25
|
1.5e-07
|
|
Astro
|
ITPKB
|
1,209
|
1
|
226,631
|
226,740
|
1.16
|
0.03
|
5.22
|
1.8e-07
|
|
Astro
|
FLRT2
|
1,319
|
14
|
85,530
|
85,655
|
1.15
|
0.03
|
5.14
|
2.7e-07
|
|
Astro
|
TNC
|
137
|
9
|
115,019
|
115,119
|
1.51
|
0.12
|
5.14
|
2.8e-07
|
|
Astro
|
SYTL4
|
209
|
X
|
100,674
|
100,733
|
1.40
|
0.09
|
5.08
|
3.7e-07
|
|
Astro
|
RHOBTB3
|
1,335
|
5
|
95,713
|
95,825
|
1.15
|
0.03
|
5.06
|
4.2e-07
|
|
Astro
|
PARD3
|
2,625
|
10
|
34,109
|
34,816
|
1.10
|
0.02
|
5.03
|
4.9e-07
|
|
Astro
|
BAZ2B
|
1,427
|
2
|
159,318
|
159,617
|
1.14
|
0.03
|
5.01
|
5.5e-07
|
|
Astro
|
SON
|
1,390
|
21
|
33,543
|
33,578
|
1.14
|
0.03
|
4.97
|
6.5e-07
|
|
Astro
|
PDE4DIP
|
2,163
|
1
|
148,808
|
149,049
|
1.11
|
0.02
|
4.96
|
6.9e-07
|
|
Astro
|
MAML2
|
2,319
|
11
|
95,976
|
96,344
|
1.11
|
0.02
|
4.92
|
8.6e-07
|
|
Astro
|
LPIN1
|
863
|
2
|
11,677
|
11,828
|
1.18
|
0.04
|
4.90
|
9.5e-07
|
|
Astro
|
TENM4
|
396
|
11
|
78,652
|
79,442
|
1.27
|
0.06
|
4.89
|
1.0e-06
|
|
Endo
|
B2M
|
233
|
15
|
44,711
|
44,719
|
2.88
|
0.18
|
16.74
|
6.7e-63
|
|
Endo
|
MT2A
|
154
|
16
|
56,608
|
56,610
|
2.56
|
0.20
|
12.35
|
5.1e-35
|
|
Endo
|
TMSB10
|
156
|
2
|
84,905
|
84,907
|
2.46
|
0.19
|
11.86
|
1.9e-32
|
|
Endo
|
CLDN5
|
130
|
22
|
19,523
|
19,528
|
2.59
|
0.21
|
11.57
|
5.6e-31
|
|
Endo
|
IFITM3
|
107
|
11
|
319
|
328
|
2.39
|
0.21
|
9.76
|
1.6e-22
|
|
Endo
|
HLA-B
|
102
|
6
|
31,269
|
31,358
|
2.34
|
0.21
|
9.33
|
1.1e-20
|
|
Endo
|
BSG
|
87
|
19
|
571
|
584
|
2.36
|
0.23
|
8.80
|
1.4e-18
|
|
Endo
|
TMSB4X
|
129
|
X
|
12,975
|
12,978
|
2.06
|
0.17
|
8.79
|
1.5e-18
|
|
Endo
|
TSC22D1
|
83
|
13
|
44,432
|
44,578
|
2.34
|
0.23
|
8.52
|
1.5e-17
|
|
Endo
|
FLT1
|
70
|
13
|
28,300
|
28,496
|
2.40
|
0.26
|
8.22
|
2.0e-16
|
|
Endo
|
APOD
|
93
|
3
|
195,568
|
195,585
|
2.14
|
0.20
|
7.99
|
1.3e-15
|
|
Endo
|
RPL13
|
88
|
16
|
89,560
|
89,565
|
2.05
|
0.20
|
7.37
|
1.8e-13
|
|
Endo
|
RASGEF1B
|
83
|
4
|
81,426
|
82,045
|
2.05
|
0.20
|
7.23
|
4.8e-13
|
|
Endo
|
RPS19
|
84
|
19
|
41,860
|
41,873
|
2.05
|
0.20
|
7.23
|
4.9e-13
|
|
Endo
|
LINGO1
|
77
|
15
|
77,613
|
77,821
|
2.05
|
0.21
|
7.02
|
2.2e-12
|
|
Endo
|
IGFBP7
|
72
|
4
|
57,030
|
57,111
|
2.09
|
0.22
|
6.99
|
2.8e-12
|
|
Endo
|
RBMS3
|
76
|
3
|
28,574
|
30,011
|
2.05
|
0.21
|
6.98
|
2.9e-12
|
|
Endo
|
HLA-C
|
67
|
6
|
31,268
|
31,273
|
2.12
|
0.23
|
6.95
|
3.7e-12
|
|
Endo
|
DLC1
|
62
|
8
|
13,083
|
13,605
|
2.13
|
0.24
|
6.75
|
1.5e-11
|
|
Endo
|
ACTB
|
86
|
7
|
5,526
|
5,564
|
1.91
|
0.19
|
6.62
|
3.6e-11
|
|
Endo
|
PTMA
|
74
|
2
|
231,706
|
231,714
|
1.98
|
0.21
|
6.56
|
5.5e-11
|
|
Endo
|
DUSP1
|
53
|
5
|
172,768
|
172,772
|
2.17
|
0.26
|
6.51
|
7.5e-11
|
|
Endo
|
HLA-A
|
65
|
6
|
29,941
|
29,946
|
2.03
|
0.22
|
6.46
|
1.0e-10
|
|
Endo
|
EEF1A1
|
86
|
6
|
73,515
|
73,524
|
1.88
|
0.18
|
6.45
|
1.1e-10
|
|
Endo
|
RPS15
|
72
|
19
|
1,438
|
1,441
|
1.95
|
0.21
|
6.31
|
2.7e-10
|
|
Endo
|
HSP90AA1
|
82
|
14
|
102,080
|
102,140
|
1.87
|
0.19
|
6.26
|
3.9e-10
|
|
Endo
|
EIF1
|
65
|
17
|
41,688
|
41,693
|
1.96
|
0.22
|
6.14
|
8.3e-10
|
|
Endo
|
RPL13A
|
69
|
19
|
49,487
|
49,493
|
1.92
|
0.21
|
6.08
|
1.2e-09
|
|
Endo
|
EPAS1
|
54
|
2
|
46,293
|
46,387
|
2.04
|
0.24
|
6.06
|
1.4e-09
|
|
Endo
|
RPL10
|
70
|
X
|
154,389
|
154,410
|
1.91
|
0.20
|
6.05
|
1.4e-09
|
|
Endo
|
ST6GALNAC3
|
55
|
1
|
76,074
|
76,635
|
2.03
|
0.24
|
6.03
|
1.6e-09
|
|
Endo
|
IFI27
|
61
|
14
|
94,104
|
94,117
|
1.96
|
0.22
|
5.96
|
2.4e-09
|
|
Endo
|
ABCB1
|
59
|
7
|
87,503
|
87,714
|
1.97
|
0.22
|
5.95
|
2.7e-09
|
|
Endo
|
PTPRG
|
66
|
3
|
61,561
|
62,298
|
1.89
|
0.21
|
5.81
|
6.1e-09
|
|
Endo
|
SPARCL1
|
68
|
4
|
87,473
|
87,532
|
1.80
|
0.19
|
5.44
|
5.2e-08
|
|
Endo
|
RPL41
|
53
|
12
|
56,116
|
56,118
|
1.89
|
0.22
|
5.38
|
7.5e-08
|
|
Endo
|
SYNE1
|
50
|
6
|
152,121
|
152,638
|
1.91
|
0.23
|
5.35
|
9.0e-08
|
|
Endo
|
HLA-E
|
53
|
6
|
30,489
|
30,495
|
1.87
|
0.22
|
5.25
|
1.5e-07
|
|
Endo
|
MBNL1
|
53
|
3
|
152,243
|
152,466
|
1.80
|
0.21
|
4.93
|
8.1e-07
|
|
Ex
|
MTRNR2L1
|
3,241
|
17
|
22,523
|
22,525
|
1.93
|
0.03
|
37.50
|
7.7e-308
|
|
Ex
|
DHFR
|
17,260
|
5
|
80,626
|
80,655
|
1.18
|
0.01
|
21.58
|
2.7e-103
|
|
Ex
|
MTRNR2L8
|
2,829
|
11
|
10,507
|
10,510
|
1.41
|
0.03
|
18.51
|
1.6e-76
|
|
Ex
|
ARL17B
|
4,977
|
17
|
46,274
|
46,362
|
0.79
|
0.01
|
-16.56
|
1.4e-61
|
|
Ex
|
ELK1
|
5,885
|
X
|
47,635
|
47,651
|
1.21
|
0.02
|
14.63
|
1.7e-48
|
|
Ex
|
EIF5A
|
2,775
|
17
|
7,306
|
7,313
|
0.77
|
0.01
|
-14.09
|
4.5e-45
|
|
Ex
|
NIPAL2
|
8,842
|
8
|
98,189
|
98,295
|
0.86
|
0.01
|
-14.02
|
1.2e-44
|
|
Ex
|
MTRNR2L12
|
4,632
|
3
|
96,617
|
96,619
|
1.21
|
0.02
|
12.92
|
3.4e-38
|
|
Ex
|
SPDYE2
|
3,447
|
7
|
102,551
|
102,563
|
0.80
|
0.01
|
-12.91
|
4.2e-38
|
|
Ex
|
SNCG
|
4,460
|
10
|
86,958
|
86,964
|
0.83
|
0.01
|
-12.22
|
2.3e-34
|
|
Ex
|
HSPA8
|
9,252
|
11
|
123,057
|
123,064
|
1.12
|
0.01
|
11.31
|
1.1e-29
|
|
Ex
|
NNAT
|
4,573
|
20
|
37,521
|
37,524
|
1.17
|
0.02
|
10.83
|
2.5e-27
|
|
Ex
|
P2RY14
|
5,427
|
3
|
151,212
|
151,279
|
1.16
|
0.02
|
10.73
|
7.7e-27
|
|
Ex
|
LRPAP1
|
5,929
|
4
|
3,503
|
3,533
|
1.14
|
0.01
|
10.16
|
2.9e-24
|
|
Ex
|
SSTR2
|
4,969
|
17
|
73,165
|
73,177
|
1.15
|
0.02
|
9.88
|
4.9e-23
|
|
Ex
|
STAT4
|
5,406
|
2
|
191,029
|
191,152
|
0.88
|
0.01
|
-9.83
|
8.6e-23
|
|
Ex
|
CNTN6
|
2,329
|
3
|
1,092
|
1,405
|
0.82
|
0.02
|
-9.81
|
1.1e-22
|
|
Ex
|
RPH3A
|
7,851
|
12
|
112,570
|
112,899
|
0.90
|
0.01
|
-9.61
|
7.1e-22
|
|
Ex
|
ITPR2
|
6,605
|
12
|
26,335
|
26,834
|
0.89
|
0.01
|
-9.59
|
8.4e-22
|
|
Ex
|
PDE5A
|
7,744
|
4
|
119,494
|
119,629
|
0.90
|
0.01
|
-9.55
|
1.3e-21
|
|
Ex
|
SEMA3A
|
6,486
|
7
|
83,955
|
84,493
|
0.89
|
0.01
|
-9.19
|
3.8e-20
|
|
Ex
|
OR2L13
|
5,594
|
1
|
248,095
|
248,102
|
1.13
|
0.02
|
9.15
|
5.5e-20
|
|
Ex
|
PTPN14
|
2,555
|
1
|
214,348
|
214,553
|
0.84
|
0.02
|
-8.96
|
3.2e-19
|
|
Ex
|
EEF1A2
|
3,296
|
20
|
63,488
|
63,500
|
1.16
|
0.02
|
8.78
|
1.6e-18
|
|
Ex
|
LRRC37A3
|
6,259
|
17
|
64,854
|
64,920
|
0.90
|
0.01
|
-8.36
|
6.1e-17
|
|
Ex
|
PTCHD4
|
2,993
|
6
|
47,878
|
48,069
|
0.86
|
0.02
|
-8.24
|
1.7e-16
|
|
Ex
|
PCED1B
|
1,681
|
12
|
47,079
|
47,237
|
0.83
|
0.02
|
-7.83
|
5.1e-15
|
|
Ex
|
EGR1
|
1,331
|
5
|
138,465
|
138,470
|
0.81
|
0.02
|
-7.73
|
1.1e-14
|
|
Ex
|
VGF
|
2,487
|
7
|
101,162
|
101,166
|
0.86
|
0.02
|
-7.71
|
1.3e-14
|
|
Ex
|
VSTM2L
|
4,594
|
20
|
37,903
|
37,946
|
0.89
|
0.01
|
-7.61
|
2.7e-14
|
|
Ex
|
CD81
|
4,281
|
11
|
2,376
|
2,398
|
1.12
|
0.02
|
7.47
|
8.0e-14
|
|
Ex
|
NBPF11
|
1,872
|
1
|
148,102
|
148,153
|
0.84
|
0.02
|
-7.36
|
1.9e-13
|
|
Ex
|
TEF
|
4,331
|
22
|
41,367
|
41,400
|
1.12
|
0.02
|
7.28
|
3.3e-13
|
|
Ex
|
LRRC37A2
|
1,636
|
17
|
46,511
|
46,556
|
0.84
|
0.02
|
-7.08
|
1.4e-12
|
|
Ex
|
TSC22D3
|
3,996
|
X
|
107,713
|
107,778
|
1.12
|
0.02
|
7.08
|
1.4e-12
|
|
Ex
|
ADAMTS2
|
1,893
|
5
|
179,110
|
179,346
|
1.18
|
0.03
|
7.05
|
1.8e-12
|
|
Ex
|
CNGB1
|
3,271
|
16
|
57,882
|
57,972
|
1.13
|
0.02
|
6.98
|
3.0e-12
|
|
Ex
|
MSH4
|
1,641
|
1
|
75,796
|
75,914
|
1.19
|
0.03
|
6.95
|
3.6e-12
|
|
Ex
|
PLA2G4A
|
732
|
1
|
186,828
|
186,989
|
0.78
|
0.03
|
-6.94
|
3.8e-12
|
|
Ex
|
SLC38A2
|
4,492
|
12
|
46,358
|
46,373
|
1.11
|
0.02
|
6.89
|
5.4e-12
|
|
Ex
|
FOS
|
89
|
14
|
75,278
|
75,283
|
0.51
|
0.05
|
-6.89
|
5.6e-12
|
|
Ex
|
ST18
|
368
|
8
|
52,110
|
52,461
|
0.70
|
0.04
|
-6.88
|
6.2e-12
|
|
Ex
|
OTOGL
|
1,513
|
12
|
80,099
|
80,381
|
0.84
|
0.02
|
-6.83
|
8.8e-12
|
|
Ex
|
RASD2
|
1,808
|
22
|
35,540
|
35,554
|
1.17
|
0.03
|
6.55
|
5.7e-11
|
|
Ex
|
DNAJB1
|
3,696
|
19
|
14,514
|
14,530
|
1.11
|
0.02
|
6.46
|
1.1e-10
|
|
Ex
|
HRH3
|
1,074
|
20
|
62,214
|
62,221
|
1.21
|
0.04
|
6.36
|
2.0e-10
|
|
Ex
|
GPS2
|
1,668
|
17
|
7,311
|
7,316
|
1.17
|
0.03
|
6.30
|
2.9e-10
|
|
Ex
|
DUSP26
|
3,574
|
8
|
33,591
|
33,601
|
1.11
|
0.02
|
6.27
|
3.7e-10
|
|
Ex
|
DUSP6
|
696
|
12
|
89,347
|
89,353
|
0.79
|
0.03
|
-6.17
|
6.7e-10
|
|
Ex
|
PMPCB
|
3,522
|
7
|
103,297
|
103,330
|
1.11
|
0.02
|
6.12
|
9.3e-10
|
|
Ex
|
NPTX2
|
1,317
|
7
|
98,617
|
98,630
|
0.85
|
0.02
|
-6.10
|
1.1e-09
|
|
Ex
|
KCNV2
|
875
|
9
|
2,717
|
2,731
|
1.23
|
0.04
|
6.07
|
1.3e-09
|
|
Ex
|
HLA-DRB1
|
184
|
6
|
32,578
|
32,590
|
0.66
|
0.05
|
-5.96
|
2.5e-09
|
|
Ex
|
MSMO1
|
3,701
|
4
|
165,327
|
165,344
|
1.10
|
0.02
|
5.90
|
3.6e-09
|
|
Ex
|
PHLDB2
|
466
|
3
|
111,732
|
111,977
|
0.77
|
0.03
|
-5.82
|
5.7e-09
|
|
Ex
|
PCSK6
|
1,238
|
15
|
101,297
|
101,526
|
0.85
|
0.02
|
-5.81
|
6.1e-09
|
|
Ex
|
PILRB
|
2,763
|
7
|
100,352
|
100,368
|
0.90
|
0.02
|
-5.79
|
7.2e-09
|
|
Ex
|
RPRM
|
1,069
|
2
|
153,477
|
153,479
|
1.19
|
0.04
|
5.75
|
9.1e-09
|
|
Ex
|
MYOM2
|
2,043
|
8
|
2,045
|
2,166
|
0.88
|
0.02
|
-5.73
|
1.0e-08
|
|
Ex
|
YIPF6
|
2,913
|
X
|
68,498
|
68,538
|
1.11
|
0.02
|
5.71
|
1.1e-08
|
|
Ex
|
LAMP5
|
3,370
|
20
|
9,514
|
9,531
|
1.10
|
0.02
|
5.71
|
1.1e-08
|
|
Ex
|
TSPAN17
|
1,337
|
5
|
176,647
|
176,660
|
1.17
|
0.03
|
5.70
|
1.2e-08
|
|
Ex
|
IL34
|
1,963
|
16
|
70,579
|
70,661
|
1.14
|
0.03
|
5.68
|
1.4e-08
|
|
Ex
|
SYT6
|
340
|
1
|
114,089
|
114,154
|
1.35
|
0.07
|
5.67
|
1.4e-08
|
|
Ex
|
TMEM233
|
1,512
|
12
|
119,593
|
119,644
|
1.16
|
0.03
|
5.64
|
1.7e-08
|
|
Ex
|
IL1RAP
|
1,726
|
3
|
190,514
|
190,660
|
0.87
|
0.02
|
-5.59
|
2.2e-08
|
|
Ex
|
CTXN3
|
895
|
5
|
127,649
|
127,659
|
0.83
|
0.03
|
-5.56
|
2.6e-08
|
|
Ex
|
TIMP2
|
3,291
|
17
|
78,852
|
78,926
|
1.10
|
0.02
|
5.54
|
3.0e-08
|
|
Ex
|
ZDHHC2
|
2,055
|
8
|
17,156
|
17,225
|
0.89
|
0.02
|
-5.52
|
3.4e-08
|
|
Ex
|
CD24
|
583
|
6
|
106,969
|
106,976
|
1.25
|
0.05
|
5.52
|
3.4e-08
|
|
Ex
|
DUSP8
|
2,317
|
11
|
1,554
|
1,573
|
1.12
|
0.02
|
5.50
|
3.8e-08
|
|
Ex
|
IGFBP5
|
3,198
|
2
|
216,672
|
216,696
|
1.10
|
0.02
|
5.47
|
4.6e-08
|
|
Ex
|
SMAD4
|
2,183
|
18
|
51,028
|
51,086
|
1.12
|
0.02
|
5.43
|
5.5e-08
|
|
Ex
|
NR4A1
|
788
|
12
|
52,022
|
52,060
|
0.83
|
0.03
|
-5.39
|
7.2e-08
|
|
Ex
|
CD53
|
882
|
1
|
110,871
|
110,900
|
0.84
|
0.03
|
-5.37
|
7.8e-08
|
|
Ex
|
TMED2
|
2,832
|
12
|
123,584
|
123,599
|
1.11
|
0.02
|
5.36
|
8.5e-08
|
|
Ex
|
TCF7L2
|
2,481
|
10
|
112,950
|
113,168
|
0.90
|
0.02
|
-5.34
|
9.2e-08
|
|
Ex
|
HUNK
|
1,723
|
21
|
31,873
|
32,045
|
0.88
|
0.02
|
-5.29
|
1.2e-07
|
|
Ex
|
TMEM144
|
785
|
4
|
158,201
|
158,256
|
0.83
|
0.03
|
-5.28
|
1.3e-07
|
|
Ex
|
PPAT
|
1,939
|
4
|
56,393
|
56,436
|
1.13
|
0.03
|
5.26
|
1.5e-07
|
|
Ex
|
CFAP61
|
1,540
|
20
|
20,052
|
20,361
|
0.88
|
0.02
|
-5.24
|
1.6e-07
|
|
Ex
|
GRIK1
|
1,903
|
21
|
29,536
|
29,941
|
0.89
|
0.02
|
-5.22
|
1.8e-07
|
|
Ex
|
TTF2
|
1,118
|
1
|
117,060
|
117,108
|
0.86
|
0.03
|
-5.21
|
1.9e-07
|
|
Ex
|
GRIK3
|
2,112
|
1
|
36,795
|
37,035
|
1.12
|
0.02
|
5.19
|
2.1e-07
|
|
Ex
|
SPTSSB
|
1,285
|
3
|
161,344
|
161,373
|
0.87
|
0.02
|
-5.14
|
2.8e-07
|
|
Ex
|
MTRNR2L6
|
198
|
7
|
142,666
|
142,668
|
1.42
|
0.10
|
5.12
|
3.0e-07
|
|
Ex
|
COBLL1
|
1,434
|
2
|
164,653
|
164,844
|
0.88
|
0.02
|
-5.06
|
4.2e-07
|
|
Ex
|
PLD1
|
931
|
3
|
171,600
|
171,811
|
0.85
|
0.03
|
-5.06
|
4.2e-07
|
|
Ex
|
HTR4
|
2,094
|
5
|
148,451
|
148,678
|
0.90
|
0.02
|
-5.06
|
4.3e-07
|
|
Ex
|
MKNK2
|
1,395
|
19
|
2,037
|
2,052
|
1.14
|
0.03
|
5.04
|
4.7e-07
|
|
Ex
|
ZDHHC22
|
2,654
|
14
|
77,131
|
77,143
|
1.10
|
0.02
|
4.98
|
6.4e-07
|
|
Ex
|
MYO1E
|
773
|
15
|
59,132
|
59,373
|
0.84
|
0.03
|
-4.96
|
6.9e-07
|
|
Ex
|
CBFB
|
1,309
|
16
|
67,028
|
67,102
|
1.15
|
0.03
|
4.95
|
7.3e-07
|
|
Ex
|
COMMD2
|
2,506
|
3
|
149,738
|
149,753
|
1.10
|
0.02
|
4.94
|
7.9e-07
|
|
Ex
|
NEDD9
|
923
|
6
|
11,183
|
11,383
|
0.85
|
0.03
|
-4.92
|
8.9e-07
|
|
Ex
|
CREG1
|
2,367
|
1
|
167,529
|
167,554
|
1.11
|
0.02
|
4.90
|
9.7e-07
|
|
In
|
MTRNR2L1
|
732
|
17
|
22,523
|
22,525
|
1.83
|
0.07
|
16.59
|
7.7e-62
|
|
In
|
DHFR
|
4,437
|
5
|
80,626
|
80,655
|
1.20
|
0.02
|
12.16
|
4.9e-34
|
|
In
|
RASGEF1B
|
6,371
|
4
|
81,426
|
82,045
|
1.13
|
0.01
|
9.71
|
2.8e-22
|
|
In
|
MTRNR2L8
|
761
|
11
|
10,507
|
10,510
|
1.40
|
0.05
|
9.36
|
8.1e-21
|
|
In
|
SLC26A3
|
3,477
|
7
|
107,765
|
107,804
|
1.17
|
0.02
|
9.32
|
1.1e-20
|
|
In
|
IQCJ-SCHIP1
|
4,990
|
3
|
158,962
|
159,898
|
1.12
|
0.02
|
8.21
|
2.1e-16
|
|
In
|
PCSK1N
|
5,724
|
X
|
48,831
|
48,836
|
1.11
|
0.01
|
7.89
|
3.1e-15
|
|
In
|
LINGO1
|
5,398
|
15
|
77,613
|
77,821
|
1.10
|
0.02
|
7.33
|
2.3e-13
|
|
In
|
ARL17B
|
805
|
17
|
46,274
|
46,362
|
0.78
|
0.03
|
-7.25
|
4.0e-13
|
|
In
|
CLU
|
2,787
|
8
|
27,596
|
27,615
|
1.15
|
0.02
|
7.17
|
7.3e-13
|
|
In
|
MTRNR2L12
|
1,121
|
3
|
96,617
|
96,619
|
1.22
|
0.04
|
6.62
|
3.7e-11
|
|
In
|
EIF5A
|
369
|
17
|
7,306
|
7,313
|
0.72
|
0.04
|
-6.54
|
6.2e-11
|
|
In
|
FTL
|
4,234
|
19
|
48,965
|
48,967
|
1.10
|
0.02
|
6.22
|
5.0e-10
|
|
In
|
CENPP
|
626
|
9
|
92,325
|
92,621
|
0.80
|
0.03
|
-5.75
|
8.8e-09
|
|
In
|
SNCG
|
1,700
|
10
|
86,958
|
86,964
|
0.88
|
0.02
|
-5.23
|
1.7e-07
|
|
Microglia
|
SPP1
|
1,391
|
4
|
87,975
|
87,984
|
1.58
|
0.04
|
17.12
|
1.0e-65
|
|
Microglia
|
PLXDC2
|
2,931
|
10
|
19,816
|
20,290
|
1.28
|
0.02
|
13.26
|
3.8e-40
|
|
Microglia
|
SLC1A3
|
1,513
|
5
|
36,606
|
36,689
|
1.37
|
0.04
|
12.38
|
3.4e-35
|
|
Microglia
|
RASGEF1B
|
439
|
4
|
81,426
|
82,045
|
1.59
|
0.07
|
9.92
|
3.5e-23
|
|
Microglia
|
APOE
|
842
|
19
|
44,905
|
44,910
|
1.39
|
0.05
|
9.67
|
4.0e-22
|
|
Microglia
|
MBNL1
|
737
|
3
|
152,243
|
152,466
|
1.39
|
0.05
|
9.11
|
8.0e-20
|
|
Microglia
|
DOCK8
|
1,064
|
9
|
214
|
466
|
1.31
|
0.04
|
8.80
|
1.4e-18
|
|
Microglia
|
HS3ST4
|
1,026
|
16
|
25,691
|
26,138
|
1.31
|
0.04
|
8.65
|
5.1e-18
|
|
Microglia
|
FKBP5
|
701
|
6
|
35,573
|
35,729
|
1.38
|
0.05
|
8.64
|
5.5e-18
|
|
Microglia
|
FRMD4A
|
2,031
|
10
|
13,643
|
14,463
|
1.21
|
0.03
|
8.63
|
5.9e-18
|
|
Microglia
|
RPS19
|
519
|
19
|
41,860
|
41,873
|
1.44
|
0.06
|
8.51
|
1.7e-17
|
|
Microglia
|
CACNA1A
|
302
|
19
|
13,206
|
13,634
|
1.60
|
0.09
|
8.45
|
3.0e-17
|
|
Microglia
|
ARHGAP24
|
1,230
|
4
|
85,475
|
86,003
|
1.26
|
0.04
|
8.30
|
1.1e-16
|
|
Microglia
|
FTL
|
986
|
19
|
48,965
|
48,967
|
1.29
|
0.04
|
7.97
|
1.5e-15
|
|
Microglia
|
DOCK10
|
545
|
2
|
224,765
|
225,043
|
1.39
|
0.06
|
7.89
|
3.0e-15
|
|
Microglia
|
MEF2C
|
1,291
|
5
|
88,717
|
88,905
|
1.24
|
0.03
|
7.74
|
9.9e-15
|
|
Microglia
|
HDAC9
|
812
|
7
|
18,086
|
19,003
|
1.31
|
0.05
|
7.73
|
1.0e-14
|
|
Microglia
|
UBE2E2
|
660
|
3
|
23,203
|
23,592
|
1.34
|
0.05
|
7.55
|
4.5e-14
|
|
Microglia
|
FOXN3
|
1,091
|
14
|
89,124
|
89,620
|
1.25
|
0.04
|
7.52
|
5.5e-14
|
|
Microglia
|
FMN1
|
439
|
15
|
32,765
|
33,195
|
1.42
|
0.07
|
7.51
|
5.8e-14
|
|
Microglia
|
ELMO1
|
974
|
7
|
36,854
|
37,450
|
1.27
|
0.04
|
7.49
|
7.0e-14
|
|
Microglia
|
LHFPL2
|
507
|
5
|
78,485
|
78,771
|
1.38
|
0.06
|
7.31
|
2.7e-13
|
|
Microglia
|
CSGALNACT1
|
558
|
8
|
19,404
|
19,759
|
1.35
|
0.06
|
7.24
|
4.3e-13
|
|
Microglia
|
DOCK4
|
1,808
|
7
|
111,726
|
112,207
|
1.18
|
0.03
|
7.24
|
4.4e-13
|
|
Microglia
|
GRID2
|
588
|
4
|
92,303
|
93,811
|
1.34
|
0.05
|
7.22
|
5.1e-13
|
|
Microglia
|
RPL13
|
391
|
16
|
89,560
|
89,565
|
1.42
|
0.07
|
7.16
|
8.3e-13
|
|
Microglia
|
LINGO1
|
383
|
15
|
77,613
|
77,821
|
1.43
|
0.07
|
7.15
|
8.8e-13
|
|
Microglia
|
MAML2
|
977
|
11
|
95,976
|
96,344
|
1.25
|
0.04
|
7.02
|
2.2e-12
|
|
Microglia
|
PICALM
|
635
|
11
|
85,957
|
86,070
|
1.31
|
0.05
|
6.96
|
3.4e-12
|
|
Microglia
|
BHLHE41
|
310
|
12
|
26,120
|
26,126
|
1.47
|
0.08
|
6.96
|
3.5e-12
|
|
Microglia
|
VSIG4
|
303
|
X
|
66,021
|
66,041
|
1.47
|
0.08
|
6.92
|
4.4e-12
|
|
Microglia
|
FGD4
|
512
|
12
|
32,399
|
32,647
|
1.35
|
0.06
|
6.91
|
4.9e-12
|
|
Microglia
|
TBC1D5
|
504
|
3
|
17,157
|
18,445
|
1.35
|
0.06
|
6.90
|
5.3e-12
|
|
Microglia
|
CSF1R
|
423
|
5
|
150,053
|
150,114
|
1.38
|
0.07
|
6.82
|
8.9e-12
|
|
Microglia
|
MEF2A
|
1,099
|
15
|
99,565
|
99,717
|
1.22
|
0.04
|
6.63
|
3.3e-11
|
|
Microglia
|
LAPTM5
|
293
|
1
|
30,732
|
30,758
|
1.46
|
0.08
|
6.62
|
3.6e-11
|
|
Microglia
|
CELF2
|
887
|
10
|
10,798
|
11,337
|
1.25
|
0.04
|
6.62
|
3.7e-11
|
|
Microglia
|
SNCA
|
216
|
4
|
89,700
|
89,839
|
1.54
|
0.10
|
6.60
|
4.0e-11
|
|
Microglia
|
TMSB4X
|
855
|
X
|
12,975
|
12,978
|
1.25
|
0.04
|
6.55
|
5.8e-11
|
|
Microglia
|
SLC9A9
|
763
|
3
|
143,265
|
143,849
|
1.26
|
0.05
|
6.49
|
8.4e-11
|
|
Microglia
|
GLDN
|
306
|
15
|
51,341
|
51,409
|
1.43
|
0.08
|
6.43
|
1.2e-10
|
|
Microglia
|
SLC26A3
|
199
|
7
|
107,765
|
107,804
|
1.55
|
0.11
|
6.43
|
1.3e-10
|
|
Microglia
|
RUNX1
|
635
|
21
|
34,787
|
36,005
|
1.28
|
0.05
|
6.40
|
1.5e-10
|
|
Microglia
|
GNAQ
|
670
|
9
|
77,716
|
78,032
|
1.28
|
0.05
|
6.38
|
1.7e-10
|
|
Microglia
|
OXR1
|
696
|
8
|
106,359
|
106,753
|
1.27
|
0.05
|
6.36
|
2.0e-10
|
|
Microglia
|
CYFIP1
|
372
|
15
|
22,867
|
22,982
|
1.38
|
0.07
|
6.30
|
3.0e-10
|
|
Microglia
|
ANKRD44
|
748
|
2
|
196,967
|
197,312
|
1.25
|
0.05
|
6.21
|
5.4e-10
|
|
Microglia
|
PSAP
|
390
|
10
|
71,816
|
71,852
|
1.36
|
0.07
|
6.17
|
7.0e-10
|
|
Microglia
|
SSH2
|
883
|
17
|
29,625
|
29,931
|
1.23
|
0.04
|
6.12
|
9.3e-10
|
|
Microglia
|
NHSL1
|
204
|
6
|
138,422
|
138,693
|
1.51
|
0.10
|
6.11
|
9.7e-10
|
|
Microglia
|
RPLP1
|
286
|
15
|
69,452
|
69,457
|
1.42
|
0.08
|
6.09
|
1.1e-09
|
|
Microglia
|
SH3RF3
|
515
|
2
|
109,129
|
109,505
|
1.30
|
0.06
|
6.08
|
1.2e-09
|
|
Microglia
|
APOC1
|
125
|
19
|
44,914
|
44,920
|
1.66
|
0.14
|
6.08
|
1.2e-09
|
|
Microglia
|
TBXAS1
|
664
|
7
|
139,777
|
140,021
|
1.26
|
0.05
|
6.07
|
1.3e-09
|
|
Microglia
|
LDLRAD4
|
867
|
18
|
13,217
|
13,653
|
1.23
|
0.04
|
6.07
|
1.3e-09
|
|
Microglia
|
APBB1IP
|
997
|
10
|
26,438
|
26,568
|
1.21
|
0.04
|
5.96
|
2.5e-09
|
|
Microglia
|
ZFHX3
|
511
|
16
|
72,782
|
73,892
|
1.29
|
0.06
|
5.94
|
2.8e-09
|
|
Microglia
|
ADGRG1
|
235
|
16
|
57,610
|
57,666
|
1.45
|
0.09
|
5.94
|
2.8e-09
|
|
Microglia
|
SKAP2
|
363
|
7
|
26,667
|
26,996
|
1.35
|
0.07
|
5.92
|
3.2e-09
|
|
Microglia
|
DPYD
|
322
|
1
|
97,077
|
97,995
|
1.38
|
0.07
|
5.92
|
3.2e-09
|
|
Microglia
|
SLTM
|
163
|
15
|
58,879
|
58,934
|
1.55
|
0.12
|
5.90
|
3.6e-09
|
|
Microglia
|
MAN2A1
|
151
|
5
|
109,689
|
109,870
|
1.56
|
0.12
|
5.81
|
6.4e-09
|
|
Microglia
|
JAZF1
|
411
|
7
|
27,830
|
28,181
|
1.32
|
0.06
|
5.79
|
7.0e-09
|
|
Microglia
|
ALCAM
|
166
|
3
|
105,366
|
105,577
|
1.53
|
0.11
|
5.79
|
7.2e-09
|
|
Microglia
|
CD81
|
192
|
11
|
2,376
|
2,398
|
1.48
|
0.10
|
5.71
|
1.1e-08
|
|
Microglia
|
RPL28
|
222
|
19
|
55,385
|
55,404
|
1.44
|
0.09
|
5.69
|
1.2e-08
|
|
Microglia
|
ST6GAL1
|
1,078
|
3
|
186,930
|
187,079
|
1.19
|
0.04
|
5.64
|
1.7e-08
|
|
Microglia
|
EPB41L2
|
797
|
6
|
130,839
|
131,064
|
1.22
|
0.04
|
5.62
|
2.0e-08
|
|
Microglia
|
STARD13
|
157
|
13
|
33,103
|
33,351
|
1.53
|
0.12
|
5.60
|
2.1e-08
|
|
Microglia
|
ITPR2
|
1,031
|
12
|
26,335
|
26,834
|
1.19
|
0.04
|
5.57
|
2.6e-08
|
|
Microglia
|
ZFP36L1
|
406
|
14
|
68,787
|
68,797
|
1.31
|
0.06
|
5.56
|
2.6e-08
|
|
Microglia
|
RPL13A
|
255
|
19
|
49,487
|
49,493
|
1.40
|
0.08
|
5.54
|
3.0e-08
|
|
Microglia
|
TANC2
|
247
|
17
|
63,009
|
63,428
|
1.40
|
0.09
|
5.51
|
3.5e-08
|
|
Microglia
|
C1QC
|
320
|
1
|
22,643
|
22,649
|
1.35
|
0.07
|
5.51
|
3.6e-08
|
|
Microglia
|
ZEB2
|
620
|
2
|
144,364
|
144,522
|
1.24
|
0.05
|
5.51
|
3.7e-08
|
|
Microglia
|
TAB2
|
378
|
6
|
149,218
|
149,412
|
1.32
|
0.07
|
5.50
|
3.7e-08
|
|
Microglia
|
ACTB
|
334
|
7
|
5,526
|
5,564
|
1.34
|
0.07
|
5.47
|
4.4e-08
|
|
Microglia
|
HSP90AA1
|
420
|
14
|
102,080
|
102,140
|
1.30
|
0.06
|
5.46
|
4.9e-08
|
|
Microglia
|
PNISR
|
346
|
6
|
99,398
|
99,426
|
1.33
|
0.07
|
5.43
|
5.7e-08
|
|
Microglia
|
AUTS2
|
319
|
7
|
69,598
|
70,794
|
1.34
|
0.07
|
5.41
|
6.5e-08
|
|
Microglia
|
EIF4G3
|
414
|
1
|
20,806
|
21,177
|
1.30
|
0.06
|
5.39
|
7.2e-08
|
|
Microglia
|
SRGAP2
|
956
|
1
|
206,203
|
206,465
|
1.19
|
0.04
|
5.38
|
7.4e-08
|
|
Microglia
|
HLA-B
|
231
|
6
|
31,269
|
31,358
|
1.40
|
0.09
|
5.34
|
9.1e-08
|
|
Microglia
|
IFNGR1
|
254
|
6
|
137,197
|
137,220
|
1.37
|
0.08
|
5.24
|
1.6e-07
|
|
Microglia
|
LPCAT2
|
389
|
16
|
55,509
|
55,587
|
1.30
|
0.06
|
5.23
|
1.7e-07
|
|
Microglia
|
P2RY12
|
357
|
3
|
151,336
|
151,385
|
1.31
|
0.07
|
5.21
|
1.9e-07
|
|
Microglia
|
RPS27A
|
203
|
2
|
55,231
|
55,236
|
1.42
|
0.10
|
5.19
|
2.1e-07
|
|
Microglia
|
N4BP2L2
|
382
|
13
|
32,432
|
32,539
|
1.29
|
0.06
|
5.16
|
2.4e-07
|
|
Microglia
|
FOXP1
|
349
|
3
|
70,952
|
71,584
|
1.31
|
0.07
|
5.16
|
2.4e-07
|
|
Microglia
|
SPIDR
|
287
|
8
|
47,260
|
47,737
|
1.34
|
0.08
|
5.16
|
2.4e-07
|
|
Microglia
|
SHTN1
|
290
|
10
|
116,881
|
117,127
|
1.34
|
0.08
|
5.13
|
2.9e-07
|
|
Microglia
|
CD74
|
709
|
5
|
150,400
|
150,413
|
1.21
|
0.04
|
5.09
|
3.5e-07
|
|
Microglia
|
BNC2
|
311
|
9
|
16,409
|
16,871
|
1.32
|
0.07
|
5.09
|
3.5e-07
|
|
Microglia
|
TCF12
|
579
|
15
|
56,918
|
57,300
|
1.23
|
0.05
|
5.09
|
3.6e-07
|
|
Microglia
|
RAP1A
|
295
|
1
|
111,542
|
111,717
|
1.33
|
0.08
|
5.07
|
3.9e-07
|
|
Microglia
|
DTNA
|
193
|
18
|
34,493
|
34,892
|
1.42
|
0.10
|
5.07
|
3.9e-07
|
|
Microglia
|
MED13L
|
553
|
12
|
115,957
|
116,278
|
1.24
|
0.05
|
5.07
|
4.0e-07
|
|
Microglia
|
SLC8A1
|
799
|
2
|
40,097
|
40,612
|
1.19
|
0.04
|
5.06
|
4.2e-07
|
|
Microglia
|
MYO1E
|
155
|
15
|
59,132
|
59,373
|
1.47
|
0.11
|
5.05
|
4.4e-07
|
|
Microglia
|
SORL1
|
688
|
11
|
121,452
|
121,634
|
1.21
|
0.05
|
5.03
|
4.8e-07
|
|
Microglia
|
ARHGAP15
|
658
|
2
|
143,091
|
143,769
|
1.21
|
0.05
|
5.03
|
5.0e-07
|
|
Microglia
|
ANKRD12
|
208
|
18
|
9,136
|
9,286
|
1.40
|
0.09
|
5.01
|
5.4e-07
|
|
Microglia
|
TMSB10
|
236
|
2
|
84,905
|
84,907
|
1.37
|
0.09
|
5.01
|
5.5e-07
|
|
Microglia
|
MAML3
|
639
|
4
|
139,716
|
140,155
|
1.22
|
0.05
|
5.01
|
5.6e-07
|
|
Microglia
|
ATM
|
333
|
11
|
108,222
|
108,370
|
1.31
|
0.07
|
5.00
|
5.7e-07
|
|
Microglia
|
SAMD12
|
137
|
8
|
118,189
|
118,623
|
1.49
|
0.12
|
4.97
|
6.8e-07
|
|
Microglia
|
SIK3
|
246
|
11
|
116,843
|
117,099
|
1.36
|
0.08
|
4.96
|
7.0e-07
|
|
Microglia
|
ZFP36L2
|
307
|
2
|
43,222
|
43,227
|
1.32
|
0.07
|
4.96
|
7.2e-07
|
|
Microglia
|
WWOX
|
404
|
16
|
78,099
|
79,213
|
1.27
|
0.06
|
4.94
|
7.9e-07
|
|
Microglia
|
TNRC6B
|
343
|
22
|
40,044
|
40,336
|
1.30
|
0.07
|
4.94
|
7.9e-07
|
|
Microglia
|
DIAPH2
|
595
|
X
|
96,684
|
97,605
|
1.22
|
0.05
|
4.93
|
8.0e-07
|
|
Microglia
|
FHIT
|
567
|
3
|
59,747
|
61,252
|
1.23
|
0.05
|
4.93
|
8.2e-07
|
|
Microglia
|
C3
|
500
|
19
|
6,677
|
6,731
|
1.24
|
0.05
|
4.92
|
8.7e-07
|
|
Microglia
|
ARMC9
|
100
|
2
|
231,198
|
231,377
|
1.57
|
0.14
|
4.89
|
1.0e-06
|
|
Microglia
|
GPATCH2L
|
150
|
14
|
76,151
|
76,255
|
1.46
|
0.11
|
4.89
|
1.0e-06
|
|
Oligo
|
NTM
|
7,395
|
11
|
131,370
|
132,337
|
1.15
|
0.01
|
11.70
|
1.2e-31
|
|
Oligo
|
ARL17B
|
382
|
17
|
46,274
|
46,362
|
0.60
|
0.03
|
-10.22
|
1.6e-24
|
|
Oligo
|
HSPA1B
|
461
|
6
|
31,827
|
31,831
|
0.63
|
0.03
|
-10.06
|
8.2e-24
|
|
Oligo
|
TLE4
|
3,345
|
9
|
79,571
|
79,727
|
1.14
|
0.02
|
7.82
|
5.5e-15
|
|
Oligo
|
PRKX
|
573
|
X
|
3,604
|
3,714
|
1.36
|
0.06
|
7.39
|
1.5e-13
|
|
Oligo
|
CHRM5
|
625
|
15
|
33,968
|
34,068
|
0.75
|
0.03
|
-7.16
|
8.1e-13
|
|
Oligo
|
ABCA6
|
651
|
17
|
69,078
|
69,142
|
1.30
|
0.05
|
6.76
|
1.4e-11
|
|
Oligo
|
PTPRM
|
831
|
18
|
7,566
|
8,407
|
1.26
|
0.04
|
6.66
|
2.7e-11
|
|
Oligo
|
ADGRL3
|
2,857
|
4
|
61,201
|
62,079
|
0.88
|
0.02
|
-6.59
|
4.4e-11
|
|
Oligo
|
ZNF365
|
2,198
|
10
|
62,374
|
62,481
|
1.15
|
0.02
|
6.50
|
8.1e-11
|
|
Oligo
|
KCNIP4
|
1,472
|
4
|
20,728
|
21,949
|
1.18
|
0.03
|
6.38
|
1.8e-10
|
|
Oligo
|
ADAMTS18
|
618
|
16
|
77,247
|
77,436
|
1.27
|
0.05
|
6.11
|
9.9e-10
|
|
Oligo
|
HSD11B1
|
375
|
1
|
209,686
|
209,735
|
0.74
|
0.04
|
-5.93
|
3.0e-09
|
|
Oligo
|
LURAP1L
|
457
|
9
|
12,775
|
12,824
|
1.31
|
0.06
|
5.89
|
3.9e-09
|
|
Oligo
|
FKBP5
|
1,885
|
6
|
35,573
|
35,729
|
1.14
|
0.03
|
5.88
|
4.0e-09
|
|
Oligo
|
RHOBTB1
|
1,289
|
10
|
60,869
|
61,002
|
1.17
|
0.03
|
5.65
|
1.6e-08
|
|
Oligo
|
CPQ
|
2,658
|
8
|
96,645
|
97,150
|
1.11
|
0.02
|
5.61
|
2.0e-08
|
|
Oligo
|
LAMA2
|
2,688
|
6
|
128,883
|
129,517
|
1.11
|
0.02
|
5.52
|
3.4e-08
|
|
Oligo
|
PDK4
|
1,037
|
7
|
95,583
|
95,597
|
1.18
|
0.04
|
5.46
|
4.9e-08
|
|
Oligo
|
CARNS1
|
1,529
|
11
|
67,414
|
67,426
|
0.87
|
0.02
|
-5.30
|
1.2e-07
|
|
Oligo
|
LIFR
|
1,840
|
5
|
38,474
|
38,609
|
1.13
|
0.03
|
5.26
|
1.4e-07
|
|
Oligo
|
HSPA1A
|
2,228
|
6
|
31,815
|
31,818
|
0.90
|
0.02
|
-5.23
|
1.7e-07
|
|
Oligo
|
MDGA2
|
1,052
|
14
|
46,839
|
47,676
|
1.17
|
0.04
|
5.07
|
4.0e-07
|
|
Oligo
|
MT3
|
1,287
|
16
|
56,589
|
56,592
|
1.15
|
0.03
|
5.04
|
4.6e-07
|
|
Oligo
|
NKX6-2
|
1,677
|
10
|
132,783
|
132,787
|
1.13
|
0.03
|
5.04
|
4.6e-07
|
|
Oligo
|
PTPN13
|
1,448
|
4
|
86,594
|
86,816
|
1.14
|
0.03
|
5.01
|
5.3e-07
|
|
Oligo
|
DCC
|
855
|
18
|
52,340
|
53,536
|
1.18
|
0.04
|
4.99
|
6.1e-07
|
|
Oligo
|
SORCS2
|
851
|
4
|
7,192
|
7,743
|
1.18
|
0.04
|
4.99
|
6.1e-07
|
|
Oligo
|
TTC3
|
1,825
|
21
|
37,073
|
37,204
|
1.12
|
0.03
|
4.90
|
9.7e-07
|
|
OPC
|
DSCAM
|
8,292
|
21
|
40,010
|
40,848
|
1.12
|
0.01
|
10.30
|
6.8e-25
|
|
OPC
|
LRRC4C
|
7,942
|
11
|
40,114
|
41,460
|
1.10
|
0.01
|
8.86
|
8.2e-19
|
|
OPC
|
LRP1B
|
7,092
|
2
|
140,231
|
142,132
|
1.10
|
0.01
|
8.17
|
3.0e-16
|
|
OPC
|
NOVA1
|
3,192
|
14
|
26,443
|
26,599
|
1.15
|
0.02
|
7.95
|
1.9e-15
|
|
OPC
|
NLGN1
|
5,979
|
3
|
173,396
|
174,287
|
1.11
|
0.01
|
7.75
|
9.1e-15
|
|
OPC
|
PTPRZ1
|
4,661
|
7
|
121,873
|
122,063
|
1.12
|
0.02
|
7.70
|
1.3e-14
|
|
OPC
|
LINGO1
|
1,267
|
15
|
77,613
|
77,821
|
1.22
|
0.03
|
7.08
|
1.4e-12
|
|
OPC
|
VCAN
|
3,832
|
5
|
83,471
|
83,583
|
1.12
|
0.02
|
7.06
|
1.6e-12
|
|
OPC
|
NTM
|
5,256
|
11
|
131,370
|
132,337
|
1.10
|
0.02
|
6.97
|
3.1e-12
|
|
OPC
|
NRG3
|
2,130
|
10
|
81,875
|
82,988
|
1.16
|
0.02
|
6.80
|
1.1e-11
|
|
OPC
|
RASGEF1B
|
1,293
|
4
|
81,426
|
82,045
|
1.20
|
0.03
|
6.74
|
1.6e-11
|
|
OPC
|
MAML2
|
2,153
|
11
|
95,976
|
96,344
|
1.15
|
0.02
|
6.41
|
1.5e-10
|
|
OPC
|
FGF12
|
2,740
|
3
|
192,139
|
192,768
|
1.13
|
0.02
|
6.31
|
2.7e-10
|
|
OPC
|
OLIG1
|
1,459
|
21
|
33,070
|
33,073
|
1.18
|
0.03
|
6.23
|
4.6e-10
|
|
OPC
|
KAZN
|
2,738
|
1
|
13,892
|
15,119
|
1.12
|
0.02
|
5.89
|
3.8e-09
|
|
OPC
|
SLC26A3
|
550
|
7
|
107,765
|
107,804
|
1.26
|
0.05
|
5.54
|
3.1e-08
|
|
OPC
|
ATRNL1
|
2,230
|
10
|
115,093
|
115,949
|
1.12
|
0.02
|
5.32
|
1.0e-07
|
|
OPC
|
FHIT
|
2,169
|
3
|
59,747
|
61,252
|
1.12
|
0.02
|
5.23
|
1.7e-07
|
|
OPC
|
PPP2R2B
|
1,949
|
5
|
146,581
|
147,085
|
1.12
|
0.03
|
5.10
|
3.4e-07
|
|
OPC
|
NCAM1
|
2,059
|
11
|
112,961
|
113,279
|
1.12
|
0.02
|
5.01
|
5.4e-07
|
|
OPC
|
ZBTB20
|
2,699
|
3
|
114,314
|
115,148
|
1.10
|
0.02
|
5.01
|
5.5e-07
|
|
Per
|
HSP90AA1
|
164
|
14
|
102,080
|
102,140
|
4.66
|
0.35
|
20.75
|
1.1e-95
|